rs10501031

Variant names:

• chr11-25995267-A-T
• rs10501031

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0665 in 152,218 control chromosomes in the GnomAD database, including 744 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.066 (744 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0664 AC: 10107 AN: 152100 Hom.: 740 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0373

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.0335

Gnomad SAS AF: 0.0488

Gnomad FIN AF: 0.00386

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0584

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0665 AC: 10122 AN: 152218 Hom.: 744 Cov.: 33 AF XY: 0.0645 AC XY: 4803 AN XY: 74442

African (AFR) AF: 0.182 AC: 7575 AN: 41516

American (AMR) AF: 0.0372 AC: 569 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3468

East Asian (EAS) AF: 0.0334 AC: 173 AN: 5184

South Asian (SAS) AF: 0.0489 AC: 236 AN: 4828

European-Finnish (FIN) AF: 0.00386 AC: 41 AN: 10612

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0163 AC: 1107 AN: 68002

Other (OTH) AF: 0.0578 AC: 122 AN: 2112

Alfa AF: 0.0441 Hom.: 54

Bravo AF: 0.0720

Asia WGS AF: 0.0370 AC: 128 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.80
PhyloP100		-0.026

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10501031; hg19: chr11-26016814;